<!DOCTYPE html>

<html>

<head>

<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />

<meta name="viewport" content="width=device-width, initial-scale=1" />



<title>Using renv with Docker</title>

<script src="data:application/javascript;base64,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"></script>

<style type="text/css">
  code{white-space: pre-wrap;}
  span.smallcaps{font-variant: small-caps;}
  span.underline{text-decoration: underline;}
  div.column{display: inline-block; vertical-align: top; width: 50%;}
  div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
  ul.task-list{list-style: none;}
    </style>


<style type="text/css">
  code {
    white-space: pre;
  }
  .sourceCode {
    overflow: visible;
  }
</style>
<style type="text/css" data-origin="pandoc">
pre > code.sourceCode { white-space: pre; position: relative; }
pre > code.sourceCode > span { display: inline-block; line-height: 1.25; }
pre > code.sourceCode > span:empty { height: 1.2em; }
.sourceCode { overflow: visible; }
code.sourceCode > span { color: inherit; text-decoration: inherit; }
div.sourceCode { margin: 1em 0; }
pre.sourceCode { margin: 0; }
@media screen {
div.sourceCode { overflow: auto; }
}
@media print {
pre > code.sourceCode { white-space: pre-wrap; }
pre > code.sourceCode > span { text-indent: -5em; padding-left: 5em; }
}
pre.numberSource code
  { counter-reset: source-line 0; }
pre.numberSource code > span
  { position: relative; left: -4em; counter-increment: source-line; }
pre.numberSource code > span > a:first-child::before
  { content: counter(source-line);
    position: relative; left: -1em; text-align: right; vertical-align: baseline;
    border: none; display: inline-block;
    -webkit-touch-callout: none; -webkit-user-select: none;
    -khtml-user-select: none; -moz-user-select: none;
    -ms-user-select: none; user-select: none;
    padding: 0 4px; width: 4em;
    color: #aaaaaa;
  }
pre.numberSource { margin-left: 3em; border-left: 1px solid #aaaaaa;  padding-left: 4px; }
div.sourceCode
  {   }
@media screen {
pre > code.sourceCode > span > a:first-child::before { text-decoration: underline; }
}
code span.al { color: #ff0000; font-weight: bold; } /* Alert */
code span.an { color: #60a0b0; font-weight: bold; font-style: italic; } /* Annotation */
code span.at { color: #7d9029; } /* Attribute */
code span.bn { color: #40a070; } /* BaseN */
code span.bu { } /* BuiltIn */
code span.cf { color: #007020; font-weight: bold; } /* ControlFlow */
code span.ch { color: #4070a0; } /* Char */
code span.cn { color: #880000; } /* Constant */
code span.co { color: #60a0b0; font-style: italic; } /* Comment */
code span.cv { color: #60a0b0; font-weight: bold; font-style: italic; } /* CommentVar */
code span.do { color: #ba2121; font-style: italic; } /* Documentation */
code span.dt { color: #902000; } /* DataType */
code span.dv { color: #40a070; } /* DecVal */
code span.er { color: #ff0000; font-weight: bold; } /* Error */
code span.ex { } /* Extension */
code span.fl { color: #40a070; } /* Float */
code span.fu { color: #06287e; } /* Function */
code span.im { } /* Import */
code span.in { color: #60a0b0; font-weight: bold; font-style: italic; } /* Information */
code span.kw { color: #007020; font-weight: bold; } /* Keyword */
code span.op { color: #666666; } /* Operator */
code span.ot { color: #007020; } /* Other */
code span.pp { color: #bc7a00; } /* Preprocessor */
code span.sc { color: #4070a0; } /* SpecialChar */
code span.ss { color: #bb6688; } /* SpecialString */
code span.st { color: #4070a0; } /* String */
code span.va { color: #19177c; } /* Variable */
code span.vs { color: #4070a0; } /* VerbatimString */
code span.wa { color: #60a0b0; font-weight: bold; font-style: italic; } /* Warning */

</style>
<script>
// apply pandoc div.sourceCode style to pre.sourceCode instead
(function() {
  var sheets = document.styleSheets;
  for (var i = 0; i < sheets.length; i++) {
    if (sheets[i].ownerNode.dataset["origin"] !== "pandoc") continue;
    try { var rules = sheets[i].cssRules; } catch (e) { continue; }
    for (var j = 0; j < rules.length; j++) {
      var rule = rules[j];
      // check if there is a div.sourceCode rule
      if (rule.type !== rule.STYLE_RULE || rule.selectorText !== "div.sourceCode") continue;
      var style = rule.style.cssText;
      // check if color or background-color is set
      if (rule.style.color === '' && rule.style.backgroundColor === '') continue;
      // replace div.sourceCode by a pre.sourceCode rule
      sheets[i].deleteRule(j);
      sheets[i].insertRule('pre.sourceCode{' + style + '}', j);
    }
  }
})();
</script>




<link rel="stylesheet" href="data:text/css,body%20%7B%0Abackground%2Dcolor%3A%20%23fff%3B%0Amargin%3A%201em%20auto%3B%0Amax%2Dwidth%3A%20700px%3B%0Aoverflow%3A%20visible%3B%0Apadding%2Dleft%3A%202em%3B%0Apadding%2Dright%3A%202em%3B%0Afont%2Dfamily%3A%20%22Open%20Sans%22%2C%20%22Helvetica%20Neue%22%2C%20Helvetica%2C%20Arial%2C%20sans%2Dserif%3B%0Afont%2Dsize%3A%2014px%3B%0Aline%2Dheight%3A%201%2E35%3B%0A%7D%0A%23TOC%20%7B%0Aclear%3A%20both%3B%0Amargin%3A%200%200%2010px%2010px%3B%0Apadding%3A%204px%3B%0Awidth%3A%20400px%3B%0Aborder%3A%201px%20solid%20%23CCCCCC%3B%0Aborder%2Dradius%3A%205px%3B%0Abackground%2Dcolor%3A%20%23f6f6f6%3B%0Afont%2Dsize%3A%2013px%3B%0Aline%2Dheight%3A%201%2E3%3B%0A%7D%0A%23TOC%20%2Etoctitle%20%7B%0Afont%2Dweight%3A%20bold%3B%0Afont%2Dsize%3A%2015px%3B%0Amargin%2Dleft%3A%205px%3B%0A%7D%0A%23TOC%20ul%20%7B%0Apadding%2Dleft%3A%2040px%3B%0Amargin%2Dleft%3A%20%2D1%2E5em%3B%0Amargin%2Dtop%3A%205px%3B%0Amargin%2Dbottom%3A%205px%3B%0A%7D%0A%23TOC%20ul%20ul%20%7B%0Amargin%2Dleft%3A%20%2D2em%3B%0A%7D%0A%23TOC%20li%20%7B%0Aline%2Dheight%3A%2016px%3B%0A%7D%0Atable%20%7B%0Amargin%3A%201em%20auto%3B%0Aborder%2Dwidth%3A%201px%3B%0Aborder%2Dcolor%3A%20%23DDDDDD%3B%0Aborder%2Dstyle%3A%20outset%3B%0Aborder%2Dcollapse%3A%20collapse%3B%0A%7D%0Atable%20th%20%7B%0Aborder%2Dwidth%3A%202px%3B%0Apadding%3A%205px%3B%0Aborder%2Dstyle%3A%20inset%3B%0A%7D%0Atable%20td%20%7B%0Aborder%2Dwidth%3A%201px%3B%0Aborder%2Dstyle%3A%20inset%3B%0Aline%2Dheight%3A%2018px%3B%0Apadding%3A%205px%205px%3B%0A%7D%0Atable%2C%20table%20th%2C%20table%20td%20%7B%0Aborder%2Dleft%2Dstyle%3A%20none%3B%0Aborder%2Dright%2Dstyle%3A%20none%3B%0A%7D%0Atable%20thead%2C%20table%20tr%2Eeven%20%7B%0Abackground%2Dcolor%3A%20%23f7f7f7%3B%0A%7D%0Ap%20%7B%0Amargin%3A%200%2E5em%200%3B%0A%7D%0Ablockquote%20%7B%0Abackground%2Dcolor%3A%20%23f6f6f6%3B%0Apadding%3A%200%2E25em%200%2E75em%3B%0A%7D%0Ahr%20%7B%0Aborder%2Dstyle%3A%20solid%3B%0Aborder%3A%20none%3B%0Aborder%2Dtop%3A%201px%20solid%20%23777%3B%0Amargin%3A%2028px%200%3B%0A%7D%0Adl%20%7B%0Amargin%2Dleft%3A%200%3B%0A%7D%0Adl%20dd%20%7B%0Amargin%2Dbottom%3A%2013px%3B%0Amargin%2Dleft%3A%2013px%3B%0A%7D%0Adl%20dt%20%7B%0Afont%2Dweight%3A%20bold%3B%0A%7D%0Aul%20%7B%0Amargin%2Dtop%3A%200%3B%0A%7D%0Aul%20li%20%7B%0Alist%2Dstyle%3A%20circle%20outside%3B%0A%7D%0Aul%20ul%20%7B%0Amargin%2Dbottom%3A%200%3B%0A%7D%0Apre%2C%20code%20%7B%0Abackground%2Dcolor%3A%20%23f7f7f7%3B%0Aborder%2Dradius%3A%203px%3B%0Acolor%3A%20%23333%3B%0Awhite%2Dspace%3A%20pre%2Dwrap%3B%20%0A%7D%0Apre%20%7B%0Aborder%2Dradius%3A%203px%3B%0Amargin%3A%205px%200px%2010px%200px%3B%0Apadding%3A%2010px%3B%0A%7D%0Apre%3Anot%28%5Bclass%5D%29%20%7B%0Abackground%2Dcolor%3A%20%23f7f7f7%3B%0A%7D%0Acode%20%7B%0Afont%2Dfamily%3A%20Consolas%2C%20Monaco%2C%20%27Courier%20New%27%2C%20monospace%3B%0Afont%2Dsize%3A%2085%25%3B%0A%7D%0Ap%20%3E%20code%2C%20li%20%3E%20code%20%7B%0Apadding%3A%202px%200px%3B%0A%7D%0Adiv%2Efigure%20%7B%0Atext%2Dalign%3A%20center%3B%0A%7D%0Aimg%20%7B%0Abackground%2Dcolor%3A%20%23FFFFFF%3B%0Apadding%3A%202px%3B%0Aborder%3A%201px%20solid%20%23DDDDDD%3B%0Aborder%2Dradius%3A%203px%3B%0Aborder%3A%201px%20solid%20%23CCCCCC%3B%0Amargin%3A%200%205px%3B%0A%7D%0Ah1%20%7B%0Amargin%2Dtop%3A%200%3B%0Afont%2Dsize%3A%2035px%3B%0Aline%2Dheight%3A%2040px%3B%0A%7D%0Ah2%20%7B%0Aborder%2Dbottom%3A%204px%20solid%20%23f7f7f7%3B%0Apadding%2Dtop%3A%2010px%3B%0Apadding%2Dbottom%3A%202px%3B%0Afont%2Dsize%3A%20145%25%3B%0A%7D%0Ah3%20%7B%0Aborder%2Dbottom%3A%202px%20solid%20%23f7f7f7%3B%0Apadding%2Dtop%3A%2010px%3B%0Afont%2Dsize%3A%20120%25%3B%0A%7D%0Ah4%20%7B%0Aborder%2Dbottom%3A%201px%20solid%20%23f7f7f7%3B%0Amargin%2Dleft%3A%208px%3B%0Afont%2Dsize%3A%20105%25%3B%0A%7D%0Ah5%2C%20h6%20%7B%0Aborder%2Dbottom%3A%201px%20solid%20%23ccc%3B%0Afont%2Dsize%3A%20105%25%3B%0A%7D%0Aa%20%7B%0Acolor%3A%20%230033dd%3B%0Atext%2Ddecoration%3A%20none%3B%0A%7D%0Aa%3Ahover%20%7B%0Acolor%3A%20%236666ff%3B%20%7D%0Aa%3Avisited%20%7B%0Acolor%3A%20%23800080%3B%20%7D%0Aa%3Avisited%3Ahover%20%7B%0Acolor%3A%20%23BB00BB%3B%20%7D%0Aa%5Bhref%5E%3D%22http%3A%22%5D%20%7B%0Atext%2Ddecoration%3A%20underline%3B%20%7D%0Aa%5Bhref%5E%3D%22https%3A%22%5D%20%7B%0Atext%2Ddecoration%3A%20underline%3B%20%7D%0A%0Acode%20%3E%20span%2Ekw%20%7B%20color%3A%20%23555%3B%20font%2Dweight%3A%20bold%3B%20%7D%20%0Acode%20%3E%20span%2Edt%20%7B%20color%3A%20%23902000%3B%20%7D%20%0Acode%20%3E%20span%2Edv%20%7B%20color%3A%20%2340a070%3B%20%7D%20%0Acode%20%3E%20span%2Ebn%20%7B%20color%3A%20%23d14%3B%20%7D%20%0Acode%20%3E%20span%2Efl%20%7B%20color%3A%20%23d14%3B%20%7D%20%0Acode%20%3E%20span%2Ech%20%7B%20color%3A%20%23d14%3B%20%7D%20%0Acode%20%3E%20span%2Est%20%7B%20color%3A%20%23d14%3B%20%7D%20%0Acode%20%3E%20span%2Eco%20%7B%20color%3A%20%23888888%3B%20font%2Dstyle%3A%20italic%3B%20%7D%20%0Acode%20%3E%20span%2Eot%20%7B%20color%3A%20%23007020%3B%20%7D%20%0Acode%20%3E%20span%2Eal%20%7B%20color%3A%20%23ff0000%3B%20font%2Dweight%3A%20bold%3B%20%7D%20%0Acode%20%3E%20span%2Efu%20%7B%20color%3A%20%23900%3B%20font%2Dweight%3A%20bold%3B%20%7D%20%0Acode%20%3E%20span%2Eer%20%7B%20color%3A%20%23a61717%3B%20background%2Dcolor%3A%20%23e3d2d2%3B%20%7D%20%0A" type="text/css" />




</head>

<body>




<h1 class="title toc-ignore">Using renv with Docker</h1>



<p>While <code>renv</code> can help capture the state of your R library at some point in time, there are still other aspects of the system that can influence the runtime behavior of your R application. In particular, the same R code can produce different results depending on:</p>
<ul>
<li>The operating system in use,</li>
<li>The compiler flags used when R and packages are built,</li>
<li>The LAPACK / BLAS system(s) in use,</li>
<li>The versions of system libraries installed and in use,</li>
</ul>
<p>And so on. <a href="https://www.docker.com/">Docker</a> is a tool that helps solve this problem through the use of <strong>containers</strong>. Very roughly speaking, one can think of a container as a small, self-contained system within which different applications can be run. Using Docker, one can declaratively state how a container should be built (what operating system it should use, and what system software should be installed within), and use that system to run applications. (For more details, please see <a href="https://environments.rstudio.com/docker" class="uri">https://environments.rstudio.com/docker</a>.)</p>
<p>Using Docker and <code>renv</code> together, one can then ensure that both the underlying system, alongside the required R packages, are fixed and constant for a particular application.</p>
<p>The main challenges in using Docker with <code>renv</code> are:</p>
<ul>
<li>Ensuring that the <code>renv</code> cache is visible to Docker containers, and</li>
<li>Ensuring that <code>renv</code> restores the R packages as required when the container is run.</li>
</ul>
<p>This vignette will assume you are already familiar with Docker; if you are not yet familiar with Docker, the <a href="https://docs.docker.com/">Docker Documentation</a> provides a thorough introduction. To learn more about using Docker to manage R environments, visit <a href="https://environments.rstudio.com/docker.html">environments.rstudio.com</a>. We’ll discuss two strategies for using <code>renv</code> with Docker:</p>
<ol style="list-style-type: decimal">
<li>Using <code>renv</code> to install packages when the Docker image is generated;</li>
<li>Using <code>renv</code> to install packages when Docker containers are run.</li>
</ol>
<p>We’ll explore the pros and cons of each strategy.</p>
<div id="creating-docker-images-with-renv" class="section level2">
<h2>Creating Docker Images with renv</h2>
<p>With Docker, <a href="https://docs.docker.com/engine/reference/builder/">Dockerfiles</a> are used to define new images. Dockerfiles can be used to declaratively specify how a Docker image should be created. A Docker image captures the state of a machine at some point in time – e.g., an Ubuntu operating system after downloading and installing R 3.5. Docker containers can be created using that image as a base, allowing isolated applications to run using the same pre-defined machine state.</p>
<p>First, you’ll need to get <code>renv</code> installed on your Docker image. The easiest way to accomplish this is with the <code>remotes</code> package. For example:</p>
<pre><code>ENV RENV_VERSION 0.13.2
RUN R -e &quot;install.packages(&#39;remotes&#39;, repos = c(CRAN = &#39;https://cloud.r-project.org&#39;))&quot;
RUN R -e &quot;remotes::install_github(&#39;rstudio/renv@${RENV_VERSION}&#39;)&quot;</code></pre>
<p>Now, <code>renv</code> can be used to install packages on the image. If you’d like the <code>renv.lock</code> lockfile to be used to install R packages when the Docker image is built, you can include something of the form:</p>
<pre><code>WORKDIR /project
COPY renv.lock renv.lock
RUN R -e &#39;renv::restore()&#39;</code></pre>
<p>With this, <code>renv</code> will download and install packages from CRAN and other external sources as appropriate when the image is created.</p>
<p>There are two main downsides to this approach:</p>
<ol style="list-style-type: decimal">
<li><p>The set of R packages used is pre-baked into the image, so different applications or containers built from this image will either have to re-use the aforementioned set of packages, or reinstall the packages they need to update as required.</p></li>
<li><p>With this approach, the <code>renv</code> package cache will not be used. This implies that package installation through <code>renv::restore()</code> may be very slow, as all packages will have to be installed.</p></li>
</ol>
<p>Both of these issues can be solved if package installation can be deferred to container runtime.</p>
</div>
<div id="running-docker-containers-with-renv" class="section level2">
<h2>Running Docker Containers with renv</h2>
<p>If you’d like to leverage the <code>renv</code> package cache alongside Docker, then you’ll need to alter how your containers are created so that <code>renv</code> can ensure the project library is initialized before your application is run.</p>
<p>One can control the <code>renv</code> cache directory with the environment variable <code>RENV_PATHS_CACHE</code>. For example:</p>
<div class="sourceCode" id="cb3"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="fu">Sys.setenv</span>(<span class="at">RENV_PATHS_CACHE =</span> <span class="st">&quot;~/path/to/cache&quot;</span>)</span>
<span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>renv<span class="sc">:::</span><span class="fu">renv_paths_cache</span>()</span>
<span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; [1] &quot;~/path/to/cache/v5/R-4.0/x86_64-apple-darwin17.0&quot;</span></span></code></pre></div>
<p>Note that the platform and R version in use are appended to the requested cache directory. This ensures that a single directory can act a base of cached packages for multiple different platforms and R versions.</p>
<p>Next, we need to figure out how to tell the Docker containers we create to use this cache. The most common option here is to mount a directory in the container that maps to persistent storage on the host system, and then set the aforementioned <code>RENV_PATHS_CACHE</code> environment variable to point to this mount. You can specify this when the container is launched. For example, if you had a container running a Shiny application:</p>
<pre><code># the path to an renv cache on the host machine
RENV_PATHS_CACHE_HOST=/opt/local/renv/cache

# the path to the cache within the container
RENV_PATHS_CACHE_CONTAINER=/renv/cacheA

# run the container with the host cache mounted in the container
docker run --rm \
    -e &quot;RENV_PATHS_CACHE=${RENV_PATHS_CACHE_CONTAINER}&quot; \
    -v &quot;${RENV_PATHS_CACHE_HOST}:${RENV_PATHS_CACHE_CONTAINER}&quot; \
    -p 14618:14618 \
    R --vanilla -s -e &#39;renv::restore(); shiny::runApp(host = &quot;0.0.0.0&quot;, port = 14618)&#39;</code></pre>
<p>With this, any calls to <code>renv</code> APIs within the created docker container will have access to the mounted cache. The first time you run a container, <code>renv</code> will likely need to populate the cache, and so some time will be spent downloading and installing the required packages. Subsequent runs should be much faster, as <code>renv</code> will be able to reuse the global package cache.</p>
<p>The primary downside with this approach compared to the image-based approach is that it requires you to modify how containers are created, and requires a bit of extra orchestration in how containers are launched. However, once the <code>renv</code> cache is active, newly-created containers will launch very quickly, and a single image can then be used as a base for a myriad of different containers and applications, each with their own private R library.</p>
</div>
<div id="handling-the-renv-autoloader" class="section level2">
<h2>Handling the renv Autoloader</h2>
<p>When is launched within a project folder, he <code>renv</code> auto-loader (if present) will attempt to download and install <code>renv</code> into the project library. Depending on how your Docker container is configured, this could fail. For example:</p>
<pre><code>Error installing renv:
======================
ERROR: unable to create ‘/usr/local/pipe/renv/library/master/R-4.0/x86_64-pc-linux-gnu/renv’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
  running command &#39;&#39;/usr/lib/R/bin/R&#39; --vanilla CMD INSTALL -l &#39;renv/library/master/R-4.0/x86_64-pc-linux-gnu&#39; &#39;/tmp/RtmpwM7ooh/renv_0.12.2.tar.gz&#39; 2&gt;&amp;1&#39; had status 1
2: Failed to find an renv installation: the project will not be loaded.
Use `renv::activate()` to re-initialize the project.</code></pre>
<p>Bootstrapping <code>renv</code> into the project library might be un-necessary for you. If that is the case, then you can avoid this behavior by launching R with the <code>--vanilla</code> flag set; for example:</p>
<pre><code>R --vanilla -s -e &#39;renv::restore()&#39;</code></pre>
</div>



<!-- code folding -->


<!-- dynamically load mathjax for compatibility with self-contained -->
<script>
  (function () {
    var script = document.createElement("script");
    script.type = "text/javascript";
    script.src  = "https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML";
    document.getElementsByTagName("head")[0].appendChild(script);
  })();
</script>

</body>
</html>
